From 6ecdbaa25d4cad3580baa17853ef546b6f975628 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Sat, 27 Nov 2021 10:31:55 +0100
Subject: [PATCH] codeml: fix test parameters (#4216)

* codeml: fix test parameters

and make all outputs valid cheetah placeholders

* correct bump
---
 tools/codeml/codeml.xml | 46 ++++++++++++++++++++---------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/tools/codeml/codeml.xml b/tools/codeml/codeml.xml
index 1c99050f83f..4aafe4f0f54 100644
--- a/tools/codeml/codeml.xml
+++ b/tools/codeml/codeml.xml
@@ -1,4 +1,4 @@
-<tool name="codeML" id="codeml" version="@TOOL_VERSION@+galaxy1" profile="18.01">
+<tool name="codeML" id="codeml" version="@TOOL_VERSION@+galaxy2" profile="18.01">
     <description>
         Detects positive selection (paml package)
     </description>
@@ -238,13 +238,13 @@ codeml '$codeml_ctl'
 
     <outputs>
         <data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" />
-        <data format="txt" name="2ngdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
+        <data format="txt" name="twongdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
             <filter>adv['seqtype']=="1"</filter>
         </data>
-        <data format="txt" name="2ngds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
+        <data format="txt" name="twongds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
             <filter>adv['seqtype']=="1"</filter>
         </data>
-        <data format="txt" name="2ngt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
+        <data format="txt" name="twongt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
             <filter>adv['seqtype']=="1"</filter>
         </data>
         <data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/>
@@ -252,25 +252,25 @@ codeml '$codeml_ctl'
         <data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/>
         <data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/>
         <data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/>
-        <data format="txt" name="4fold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc">
+        <data format="txt" name="fourfold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc">
             <filter>adv['verbose']=="1"</filter>
         </data>
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="9">
             <conditional name="compat_model" >
                 <param name="brmodel" value="0" />
                 <param name="NSsites" value="0" />
             </conditional>
-            <param name="adv.fix_omega" value="0" />
-            <param name="adv.omega" value="0.2" />
+            <param name="adv|fix_omega" value="0" />
+            <param name="adv|omega" value="0.2" />
             <param name="RateAncestor" value="1" />
             <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
             <param name="tree" value="RAxML_bestTree" ftype="nhx" />
-            <output name="2ngdn" value="1_2ngdn" />
-            <output name="2ngds" value="1_2ngds" />
-            <output name="2ngt" value="1_2ngt" />
+            <output name="twongdn" value="1_2ngdn" />
+            <output name="twongds" value="1_2ngds" />
+            <output name="twongt" value="1_2ngt" />
             <output name="run">
                 <assert_contents>
                     <has_text text="CODONML (in paml version 4.9, March 2015)"/>
@@ -279,19 +279,19 @@ codeml '$codeml_ctl'
             </output>
             <output name="ctl" value="1_codeml.ctl" lines_diff="4" />
         </test>
-        <test>
+        <test expect_num_outputs="9">
             <conditional name="compat_model" >
                 <param name="brmodel" value="2" />
                 <param name="NSsites" value="0" />
             </conditional>
-            <param name="adv.fix_omega" value="0" />
-            <param name="adv.omega" value="0.2" />
+            <param name="adv|fix_omega" value="0" />
+            <param name="adv|omega" value="0.2" />
             <param name="RateAncestor" value="1" />
             <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
             <param name="tree" value="tree_model2" ftype="nhx" />
-            <output name="2ngdn" value="2_2ngdn" />
-            <output name="2ngds" value="2_2ngds" />
-            <output name="2ngt" value="2_2ngt" />
+            <output name="twongdn" value="2_2ngdn" />
+            <output name="twongds" value="2_2ngds" />
+            <output name="twongt" value="2_2ngt" />
             <output name="run">
                 <assert_contents>
                     <has_text text="CODONML (in paml version 4.9, March 2015)"/>
@@ -300,19 +300,19 @@ codeml '$codeml_ctl'
             </output>
             <output name="ctl" value="2_codeml.ctl" lines_diff="4" />
         </test>
-        <test>
+        <test expect_num_outputs="9">
             <conditional name="compat_model" >
                 <param name="brmodel" value="3" />
                 <param name="NSsites" value="2" />
             </conditional>
-            <param name="adv.fix_omega" value="0" />
-            <param name="adv.omega" value="0.2" />
+            <param name="adv|fix_omega" value="0" />
+            <param name="adv|omega" value="0.2" />
             <param name="RateAncestor" value="1" />
             <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
             <param name="tree" value="tree_model3" ftype="nhx" />
-            <output name="2ngdn" value="3_2ngdn" />
-            <output name="2ngds" value="3_2ngds" />
-            <output name="2ngt" value="3_2ngt" />
+            <output name="twongdn" value="3_2ngdn" />
+            <output name="twongds" value="3_2ngds" />
+            <output name="twongt" value="3_2ngt" />
             <output name="run">
                 <assert_contents>
                     <has_text text="CODONML (in paml version 4.9, March 2015)"/>